Evidence for influenza B virus lineage shifts and reassortants circulating in Thailand in 2014-2016

Genetic Reassortment in a Child Coinfected with Two Influenza B Viruses, B/Yamagata Lineage and B/Victoria-Lineage Strains

We identified a child coinfected with influenza B viruses of B/Yamagata and B/Victoria lineages, in whom we analyzed the occurrence of genetic reassortment. Plaque purification was performed using a throat swab specimen from a 9-year-old child, resulting in 34 well-isolated plaques. The genomic composition of eight gene segments (HA, NA, PB1, PB2, PA, NP, M, and NS genes) for each plaque was determined at the lineage level. Of the 34 plaques, 21 (61.8%) had B/Phuket/3073/2013 (B/Yamagata)-like sequences in all gene segments, while the other 13 (38.2%) were reassortants with B/Texas/02/2013 (B/Victoria)-like sequences in 1-5 of the 8 segments. The PB1 segment had the most B/Victoria lineage genes (23.5%; 8 of 34 plaques), while PB2 and PA had the least (2.9%; 1 of 34 plaques). Reassortants with B/Victoria lineage genes in 2-5 segments showed the same level of growth as viruses with B/Yamagata lineage genes in all segments. However, reassortants with B/Victoria lineage genes only in the NA, PB1, NP, or NS segments exhibited reduced or undetectable growth. We demonstrated that various gene reassortments occurred in a child. These results suggest that simultaneous outbreaks of two influenza B virus lineages increase genetic diversity and could promote the emergence of new epidemic strains.

Molecular characterization and evolution dynamics of influenza B viruses circulating in Germany from season 1996/1997 to 2019/2020

Influenza B viruses are responsible for significant disease burden caused by viruses of both the Yamagata- and Victoria-lineage. Since the circulating patterns of influenza B viruses in different countries vary we investigated molecular properties and evolution dynamics of influenza B viruses circulating in Germany between 1996 and 2020. A change of the dominant lineage occurred in Germany in seven seasons in over past 25 years. A total of 676 sequences of hemagglutinin coding domain 1 (HA1) and 516 sequences of neuraminidase (NA) genes of Yamagata- and Victoria-lineage viruses were analyzed using time-scaled phylogenetic tree. Phylogenetic analysis demonstrated that Yamagata-lineage viruses are more diverse than the Victoria-lineage viruses and could be divided into nine genetic groups whereas Victoria-lineage viruses presented six genetic groups. Comparative phylogenetic analyses of both the HA and NA segments together revealed a number of inter-lineage as well as inter- and intra-clade reassortants. We identified key amino acid substitutions in major HA epitopes such as in four antigenic sites and receptor-binding sites (RBS) and in the regions close to them, with most substitutions in the 120-loop of both lineage viruses. Altogether, seventeen substitutions were fixed over time within the Yamagata-lineage with twelve of them in the antigenic sites. Thirteen substitutions were identified within the Victoria-lineage, with eleven of them in the antigenic sites. Moreover, all Victoria-lineage viruses of the 2017/2018 season were characterized by a deletion of two amino acids at the position 162-163 in the antigenic site of HA1. The viruses with triple deletion Δ162-164 were found in Germany since season 2018/2019. We highlighted the interplay between substitutions in the glycosylation sites and RBS and antigenic epitope during HA evolution. The results obtained underscore the need for continuous monitoring of circulating influenza B viruses. Early detection of strains with genetic and antigenic variation is essential to predict the circulation patterns for the following season. Such information is important for the development of optimal vaccines and strategies for prevention and control of influenza.

Genome characterization and mutation analysis of human influenza A virus in Thailand

The influenza A viruses have high mutation rates and cause a serious health problem worldwide. Therefore, this study focused on genome characterization of the viruses isolated from Thai patients based on the next-generation sequencing technology. The nasal swabs were collected from patients with influenza-like illness in Thailand during 2017-2018. Then, the influenza A viruses were detected by reverse transcription-quantitative polymerase chain reaction and isolated by MDCK cells. The viral genomes were amplified and sequenced by Illumina MiSeq platform. Whole genome sequences were used for characterization, phylogenetic construction, mutation analysis and nucleotide diversity of the viruses. The result revealed that 90 samples were positive for the viruses including 44 of A/H1N1 and 46 of A/H3N2. Among these, 43 samples were successfully isolated and then the viral genomes of 25 samples were completely amplified. Finally, 17 whole genomes of the viruses (A/H1N1, n=12 and A/H3N2, n=5) were successfully sequenced with an average of 232,578 mapped reads and 1,720 genome coverage per sample. Phylogenetic analysis demonstrated that the A/H1N1 viruses were distinguishable from the recommended vaccine strains. However, the A/H3N2 viruses from this study were closely related to the recommended vaccine strains. The nonsynonymous mutations were found in all genes of both viruses, especially in HA and NA genes. The nucleotide diversity analysis revealed negative selection in the PB1, PA, hemagglutinin (HA) and neuraminidase (NA) genes of the A/H1N1 viruses. High-throughput data in this study allow for genetic characterization of circulating influenza viruses which would be crucial for preparation against pandemic and epidemic outbreaks in the future.

Epidemiology and Molecular Analyses of Influenza B Viruses in Senegal from 2010 to 2019

Influenza virus types A and B are responsible for acute viral infections that affect annually 1 billion people, with 290,000 to 650,000 deaths worldwide. In this study, we investigated the circulation of influenza B viruses over a 10-year period (2010–2019). Specimens from patients suspected of influenza infection were collected. Influenza detection was performed following RNA extraction and real-time RT-PCR. Genes coding for hemagglutinin (HA) and neuraminidase (NA) of influenza B viruses were partially sequenced, and phylogenetic analyses were carried out subsequently. During the study period, we received and tested a total of 15,156 specimens. Influenza B virus was detected in 1322 (8.7%) specimens. The mean age of influenza B positive patients was 10.9 years. When compared to reference viruses, HA genes from Senegalese circulating viruses showed deletions in the HA1 region. Phylogenetic analysis highlighted the co-circulation of B/Victoria and B/Yamagata lineage viruses with reassortant viruses. We also noted a clear seasonal pattern of circulation of influenza B viruses in Senegal.

Prevalence of antibodies against seasonal influenza A and B viruses among older adults in rural Thailand: A cross-sectional study

Assessing the seroprevalence of the high-risk individuals against the influenza virus is essential to evaluate the progress of vaccine implementation programs and establish influenza virus interventions. Herein, we identified the pre-existing cross-protection of the circulating seasonal influenza viruses among the older-aged population. A cross-sectional study was performed base on the 176 residual sera samples collected from older adults aged 60 to 95 years without a history of vaccination in rural Thailand in 2015. Sera antibody titers against influenza A and B viruses circulating between 2016 and 2019 were determined by hemagglutination inhibition assay. These findings indicated the low titers of pre-existing antibodies to circulating influenza subtypes and showed age-independent antibody titers among the old adults. Moderate seropositive rates (HAI ≥ 1:40) were observed in influenza A viruses (65.9%A(H3N2), 50.0% for A(H1N1) pdm09), and found comparatively lower rates in influenza B viruses (14% B/Yam2, 21% B/Yam3 and 25% B/Vic). Only 5% of individuals possessed broadly protective antibodies against both seasonal influenza A and B virus in this region. Our findings highlighted the low pre-existing antibodies to circulating influenza strains in the following season observed in older adults. The serological study will help inform policy-makers for health care planning and guide control measures concerning vaccination programs.

Cost-Effectiveness of Quadrivalent Versus Trivalent Influenza Vaccination in the Dutch National Influenza Prevention Program

OBJECTIVES

As of 2019, quadrivalent influenza vaccine (QIV) has replaced trivalent influenza vaccine (TIV) in the national immunization program in The Netherlands. Target groups are individuals of 60+ years of age and those with chronic diseases. The objective was to estimate the incremental break-even price of QIV over TIV at a threshold of €20 000 per quality-adjusted life-year (QALY).

METHODS

An age-structured compartmental dynamic model was adapted for The Netherlands to assess health outcomes and associated costs of vaccinating all individuals at higher risk for influenza with QIV instead of TIV over the seasons 2010 to 2018. Influenza incidence rates were derived from a global database. Other parameters (probabilities, QALYs and costs) were extracted from the literature and applied according to Dutch guidelines. A threshold of €20 000 per QALY was applied to estimate the incremental break-even prices of QIV versus TIV. Sensitivity analyses were performed to test the robustness of the model outcomes.

RESULTS

Retrospectively, vaccination with QIV instead of TIV could have prevented on average 9500 symptomatic influenza cases, 2130 outpatient visits, 84 hospitalizations, and 38 deaths per year over the seasons 2010 to 2018. This translates into 385 QALYs and 398 life-years potentially gained. On average, totals of €431 527 direct and €2 388 810 indirect costs could have been saved each year.

CONCLUSION

Using QIV over TIV during the influenza seasons 2010 to 2018 would have been cost-effective at an incremental price of maximally €3.81 (95% confidence interval, €3.26-4.31). Sensitivity analysis showed consistent findings on the incremental break-even price in the same range.

Epidemiological and evolutionary dynamics of influenza B virus in coastal Kenya as revealed by genomic analysis of strains sampled over a single season

The genomic epidemiology of influenza B virus (IBV) remains understudied in Africa despite significance to design of effective local and global control strategies. We undertook surveillance throughout 2016 in coastal Kenya, recruiting individuals presenting with acute respiratory illness at nine outpatient health facilities (any age) or admitted to the Kilifi County Hospital (<5 years old). Whole genomes were sequenced for a selected 111 positives; 94 (84.7%) of B/Victoria lineage and 17 (15.3%) of B/Yamagata lineage. Inter-lineage reassortment was detected in ten viruses; nine with B/Yamagata backbone but B/Victoria NA and NP segments and one with a B/Victoria backbone but B/Yamagata PB2, PB1, PA, and MP segments. Five phylogenomic clusters were identified among the sequenced viruses; (i), pure B/Victoria clade 1A (n = 93, 83.8%), (ii), reassortant B/Victoria clade 1A (n = 1, 0.9%), (iii), pure B/Yamagata clade 2 (n = 2, 1.8%), (iv), pure B/Yamagata clade 3 (n = 6, 5.4%), and (v), reassortant B/Yamagata clade 3 (n = 9, 8.1%). Using divergence dates and clustering patterns in the presence of global background sequences, we counted up to twenty-nine independent IBV strain introductions into the study area (∼900 km2) in 2016. Local viruses, including the reassortant B/Yamagata strains, clustered closely with viruses from neighbouring Tanzania and Uganda. Our study demonstrated that genomic analysis provides a clearer picture of locally circulating IBV diversity. The high number of IBV introductions highlights the challenge in controlling local influenza epidemics by targeted approaches, for example, sub-population vaccination or patient quarantine. The finding of divergent IBV strains co-circulating within a single season emphasises why broad immunity vaccines are the most ideal for influenza control in Kenya.

Predominance of influenza B/Yamagata lineage viruses in Bulgaria during the 2017/2018 season

In this study, we investigated the antigenic and genetic characteristics of influenza viruses circulating in Bulgaria during the 2017/2018 season. The detection and typing/subtyping of influenza viruses were performed using real-time RT-PCR. Results of antigenic characterisation, phylogenetic and amino acid sequence analyses of representative influenza strains are presented. The season was characterised by the predominance of B/Yamagata viruses, accounting for 77% of detected influenza viruses, followed by A(H1N1)pdm09 (17%), B/Victoria (3.7%) and A(H3N2) (2.4%). The sequenced B/Yamagata, B/Victoria, A(H1N1)pdm09 and A(H3N2) viruses belonged to the genetic groups 3, 1A, 6B.1 and 3C.2a1, respectively. Amino acid analysis of B/Yamagata isolates revealed the presence of three changes in haemagglutinin (HA), eight changes in neuraminidase (NA) and a number of substitutions in internal proteins compared with the B/Phucket/3073/2013 vaccine virus. Despite the amino acid changes, B/Yamagata viruses remained antigenically related to the vaccine strain. B/Victoria isolates fell into a group of viruses with double deletion (Δ162-163) in HA1. Substitutions in HA and NA sequences of B/Victoria, A(H1N1)pdm09 and A(H3N2) viruses were also identified compared with the vaccine strains, including in antigenic sites. The results of this study confirm the genetic variability of circulating influenza viruses and the need for continual antigenic and molecular surveillance.

Analysis of influenza B virus lineages and the HA1 domain of its hemagglutinin gene in Guangzhou, southern China, during 2016

Background

Few studies have analyzed influenza B virus lineages based on hemagglutinin A (HA) gene sequences in southern China. The present study analyzed the HA gene and the lineages of influenza B virus isolates from Guangzhou during 2016, and compared our results with the WHO-recommended vaccine strain.

Methods

Ninety patients with influenza B were recruited from the First Hospital of Guangzhou Medical University. Throat swab specimens of 72 patients had high viral loads. Among these 72 isolates, the HA1 domain of the HA gene in 43 randomly selected isolates was sequenced using reverse transcription-polymerase chain reaction (RT-PCR), and analyzed using MEGA 5.05.

Results

Eight of the 90 patients (8.9%) also had influenza A virus infections. Analysis of the 43 influenza B virus isolates indicated that 34 (79.1%) were from the Victoria lineage and 9 (20.9%) were from the Yamagata lineage. A comparison isolates in our Victoria lineage with the B/Brisbane/60/2008 strain indicated 12 mutation sites in the HA1 domain, 4 of which (I132V, N144D, C196S, and E198D) were in antigenic epitopes. A comparison of isolates in our Yamagata lineage with the B/Phuket/3073/2013 stain indicated 5 mutation sites in the HA1 domain, none of which was in an antigenic epitope. None of the isolates had a mutation in regions of the neuraminidase gene (NA) that are known to confer resistance to NA inhibitors.

Conclusion

In Guangzhou during 2016, most influenza B virus isolates were from the Victoria lineage, in contrast to the vaccine strain recommended by the WHO for this period.

Electronic supplementary material

The online version of this article (10.1186/s12985-018-1085-5) contains supplementary material, which is available to authorized users.

Epidemiology of seasonal influenza in the Middle East and North Africa regions, 2010-2016: Circulating influenza A and B viruses and spatial timing of epidemics

BACKGROUND

There is a limited knowledge regarding the epidemiology of influenza in Middle East and North Africa.

OBJECTIVES

We described the patterns of influenza circulation and the timing of seasonal epidemics in countries of Middle East and North Africa.

METHODS

We used virological surveillance data for 2010-2016 from the WHO FluNet database. In each country, we calculated the median proportion of cases that were caused by each virus type and subtype; determined the timing and amplitude of the primary and secondary peaks; and used linear regression models to test for spatial trends in the timing of epidemics.

RESULTS

We included 70 532 influenza cases from seventeen countries. Influenza A and B accounted for a median 76.5% and 23.5% of cases in a season and were the dominant type in 86.8% and 13.2% of seasons. The proportion of influenza A cases that were subtyped was 85.9%, while only 4.4% of influenza B cases were characterized. For most countries, influenza seasonality was similar to the Northern Hemisphere, with a single large peak between January and March; exceptions were the countries in the Arabian Peninsula and Jordan, all of which showed clear secondary peaks, and some countries had an earlier primary peak (in November-December in Bahrain and Qatar). The direction of the timing of influenza activity was east to west and south to north in 2012-2013 and 2015-2016, and west to east in 2014-2015.

CONCLUSIONS

The epidemiology of influenza is generally uniform in countries of Middle East and North Africa, with influenza B playing an important role in the seasonal disease burden.

Forty five percent of the Israeli population were infected with the influenza B Victoria virus during the winter season 2015-16

While infection with influenza A viruses has been extensively investigated, infections with influenza B viruses which are commonly categorized into the highly homologous Victoria and Yamagata lineages, are less studied, despite their considerable virulence. Here we used RT-PCR assays, hemagglutination inhibition assays and antibody titers to determine the levels of influenza B infection. We report of high influenza B Victoria virus prevalence in the 2015-16 winter season in Israel, affecting approximately half of the Israeli population. We further show that the Victoria B virus infected individuals of all ages and that it was present in the country throughout the entire winter season. The vaccine however included the inappropriate Yamagata virus. We propose that a quadrivalent vaccine, that includes both Yamagata and Victoria lineages, should be considered for future influenza vaccination.

Respiratory syncytial virus genotypes NA1, ON1, and BA9 are prevalent in Thailand, 2012-2015

Respiratory syncytial virus (RSV) causes acute lower respiratory tract infection in infants and young children worldwide. To investigate the RSV burden in Thailand over four consecutive years (January 2012 to December 2015), we screened 3,306 samples obtained from children ≤5 years old with acute respiratory tract infection using semi-nested reverse-transcription polymerase chain reaction (RT-PCR). In all, 8.4% (277/3,306) of the specimens tested positive for RSV, most of which appeared in the rainy months of July to November. We then genotyped RSV by sequencing the G glycoprotein gene and performed phylogenetic analysis to determine the RSV antigenic subgroup. The majority (57.4%, 159/277) of the RSV belonged to subgroup A (RSV-A), of which NA1 genotype was the most common in 2012 while ON1 genotype became prevalent the following year. Among samples tested positive for RSV-B subgroup B (RSV-B) (42.6%, 118/277), most were genotype BA9 (92.6%, 87/94) with some BA10 and BA-C. Predicted amino acid sequence from the partial G region showed highly conserved N-linked glycosylation site at residue N237 among all RSV-A ON1 strains (68/68), and at residues N296 (86/87) and N310 (87/87) among RSV-B BA9 strains. Positive selection of key residues combined with notable sequence variations on the G gene contributed to the continued circulation of this rapidly evolving virus.

Molecular epidemiology of influenza B virus among hospitalized pediatric patients in Northern Italy during the 2015-16 season

Background

The influenza B viruses belong to two lineages distinguished by their genetic and antigenic characteristics, which are referred to as the Yamagata and Victoria lineages, designated after their original isolates, B/Yamagata/16/88 and B/Victoria/2/87. The primary aim of this study was to evaluate the molecular characteristics of influenza B viruses circulating in a region of Northern Italy, Lombardia, during the influenza season of 2015–2016.

Methods

Influenza B virus was detected using a respiratory virus panel of assays and an influenza B-specific real-time polymerase chain reaction. The complete influenza B hemagglutinin (HA) gene was amplified and sequenced directly from clinical specimens. Phylogenetic analysis was performed using nucleotide sequences.

Results

A total of 71 hospitalized pediatric patients were influenza B positive. Phylogenetic analysis showed that the great majority of influenza B strains (66/71, 93.0%) belonged to the Victoria-lineage and were antigenically like vaccine strain (B/Brisbane/60/2008) included only in the quadrivalent vaccine. In the detected influenza B strains, a series of amino acid changes were observed in the antigenic regions: I117V, V124A, N129D, V146I, N197D, T199A, and A202T. However, only 2 amino acid changes were observed in the HA regions involved in receptor binding or in antibody recognition.

Conclusions

All the influenza B strains identified in this study belonged to the influenza B Victoria lineage not included in the trivalent vaccine commonly used by the general population during the 2015–2016 influenza season in Italy. This indicates that protection against influenza B infection in the vaccinated population was in general very poor during the 2015–2016 influenza season.